In 2020，the added value of the digital economy in Guangdong Province was about 5.2 trillion yuan，ranking first among China.Facing to the needs of building an international science and technology innovation center in the Guangdong-Hong Kong-Macao Greater Bay Area and Guangdong Province，we use 2385623 patent data from 42295 high and new tech enterprises and technology-based small and medium-sized enterprise among 21cities of Guangdong Province form 2016 to 2020 as our research sample，to evaluate the innovation level of the digital economy in Guangdong Province.The study finds that the total number of enterprises，the total number of patents and the comprehensive innovation level in the core area of the Pearl River Delta occupy an absolute advantage in the province.Among them，the innovation level of Shenzhen，Guangzhou，Dongguan，Foshan and Zhuhai rank the top five，with obvious agglomeration effect；Baoan，Nanshan，Longhua，Longgang and Huangpu ranks among the top five districts in Guangdong，and the per capital GDP of each district is positively correlated with the average innovation level of the digital economy.Among the five major industries，the digital product manufacturing industry and the digital technology application industry rank the top two，and the digital product manufacturing industry has the highest level of digital economic innovation and the most concentrated firms；those leading technology-based firms are an important force for the digital economic innovation activities in Guangdong.There is a significant pulling effect on the innovation level of various regions.We suggest to start the assessment of the digital economy innovation level in Guangdong as soon as possible，in order to promote its high-quality development，and to take the lead in the field of digital economy innovation and development.